Browse Source

ap/ncbi-toolkit: Removed.

slackware-14.2
Damien Goutte-Gattat 9 years ago
parent
commit
8461522a32
  1. 40
      ap/ncbi-toolkit/build-fixes.diff
  2. 12
      ap/ncbi-toolkit/doinst.sh
  3. 143
      ap/ncbi-toolkit/ncbi-toolkit.SlackBuild
  4. 1
      ap/ncbi-toolkit/ncbi.tar.gz.sha1
  5. 3
      ap/ncbi-toolkit/ncbirc
  6. 13
      ap/ncbi-toolkit/slack-desc

40
ap/ncbi-toolkit/build-fixes.diff

@ -1,40 +0,0 @@
diff -Naur ncbi.orig/ncbi/corelib/ncbienv.c ncbi/ncbi/corelib/ncbienv.c
--- ncbi.orig/ncbi/corelib/ncbienv.c 2007-05-04 15:43:59.000000000 +0200
+++ ncbi/ncbi/corelib/ncbienv.c 2009-03-27 01:37:01.000000000 +0100
@@ -812,6 +812,8 @@
if (fp == NULL) {
path[0] = '\0';
pth = getenv ("NCBI");
+ if (pth == NULL)
+ pth = "/etc/ncbi";
if (pth != NULL) {
Nlm_FileBuildPath(path, pth, str + 1);
fp = Ncbienv_FileOpen (path, "r");
diff -Naur ncbi.orig/ncbimake/makedis.csh ncbi/ncbi/make/makedis.csh
--- ncbi.orig/ncbi/make/makedis.csh 2008-12-30 16:15:10.000000000 +0100
+++ ncbi/ncbi/make/makedis.csh 2009-03-27 01:39:23.000000000 +0100
@@ -342,8 +342,8 @@
#
#uncomment two following lines to don't build X11 apps
-#set HAVE_OGL=0
-#set HAVE_MOTIF=0
+set HAVE_OGL=0
+set HAVE_MOTIF=0
# if $OPENGL_TARGETS (in <platform>.ncbi.mk) is defined,
# then add the appropriate flags, libraries, and binaries for OpenGL apps
diff -Naur ncbi/ncbi.orig/platform/linux-x86.ncbi.mk ncbi/ncbi/platform/linux-x86.ncbi.mk
--- ncbi.orig/ncbi/platform/linux-x86.ncbi.mk 2009-02-04 15:24:03.000000000 +0100
+++ ncbi/ncbi/platform/linux-x86.ncbi.mk 2009-03-27 01:38:18.000000000 +0100
@@ -11,8 +11,8 @@
NCBI_AR=ar
NCBI_CC = gcc -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_GNU_SOURCE
NCBI_CFLAGS1 = -c
-NCBI_LDFLAGS1 = -O3 -mcpu=pentium4
-NCBI_OPTFLAG = -O3 -mcpu=pentium4
+NCBI_LDFLAGS1 = -O2 -march=i686 -mtune=i686
+NCBI_OPTFLAG = -O2 -march=i686 -mtune=i686
NCBI_BIN_MASTER = /home/coremake/ncbi/bin
NCBI_BIN_COPY = /home/coremake/ncbi/bin
NCBI_INCDIR = /home/coremake/ncbi/include

12
ap/ncbi-toolkit/doinst.sh

@ -1,12 +0,0 @@
#!/bin/sh
config()
{
NEW="$1"
OLD="`dirname $NEW`/`basename $NEW .new`"
if [ ! -r $OLD ]; then
mv $NEW $OLD
elif [ "`cat $OLD | md5sum`" = "`cat $NEW | md5sum`" ]; then
rm $NEW
fi
}
config /etc/ncbi/ncbirc.new

143
ap/ncbi-toolkit/ncbi-toolkit.SlackBuild

@ -1,143 +0,0 @@
#!/bin/bash
# Build script for Slackware
# Copyright (C) 2008,2009,2010,2011 Damien Goutte-Gattat
#
# Redistribution and use of this script, with or without modifications,
# is permitted provided that the following conditions are met:
#
# 1. Redistributions of this script must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR AS IS'' AND ANY EXPRESS OR
# IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
# INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
# STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
# IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
# Contact: Damien Goutte-Gattat <dgouttegattat@incenp.org>
#
# Latest ncbi sourcecode is available at:
# <ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/CURRENT>.
# Source package infos
NAMESRC=${NAMESRC:-ncbi}
VERSION=${VERSION:-6.1}
ARCHIVE=${ARCHIVE:-$NAMESRC.tar.gz}
WGET=${WGET:-ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/20090809/$ARCHIVE}
# Built package infos
NAMEPKG=${NAMEPKG:-ncbi-toolkit}
BUILD=${BUILD:-1GGD}
ARCH=${ARCH:-$(uname -m | sed 's/^i.86$/i486/;s/^arm.*/arm/')}
EXT=${EXT:-txz}
# Directories
TMP=${TMP:-/tmp}
OUT=${OUT:-$TMP/build}
PKG=${PKG:-$OUT/$NAMEPKG}
CWD=$(pwd)
set -e # Quit if a command returns non-zero
# Sanity checks
if [ $UID -eq 0 ]; then
echo "You should NOT run this script as ROOT!"
exit 1
fi
if [ ! -d $TMP ]; then
echo "$TMP does not exist or is not a directory!"
exit 1
fi
# Library directory
case "$ARCH" in
x86_64)
LIBDIRSUFFIX="64"
;;
*)
LIBDIRSUFFIX=""
;;
esac
# Get and verify the source archive
if [ ! -r $ARCHIVE ]; then
wget -c -O $ARCHIVE.part "$WGET"
mv $ARCHIVE.part $ARCHIVE
fi
sha1sum -c $ARCHIVE.sha1
NAME=$(tar ft $ARCHIVE | head -n 1 | cut -d / -f 1)
# Build
cd $TMP
echo "Building $ARCHIVE..."
mkdir ncbi && cd ncbi
tar xf $CWD/$ARCHIVE
patch -p 1 < $CWD/build-fixes.diff
./ncbi/make/makedis.csh
# Install binaries and include files
mkdir -p $PKG/usr/include
cp -aL ncbi/bin $PKG/usr/bin
rm $PKG/usr/bin/{demo*,dosimple,test*}
mv $PKG/usr/bin/wblast2.REAL $PKG/usr/bin/wblast2
mv $PKG/usr/bin/wblast2_cs.REAL $PKG/usr/bin/wblast2_cs
cp -aL ncbi/lib $PKG/usr/lib$LIBDIRSUFFIX
strip --strip-unneeded $PKG/usr/bin/* $PKG/usr/lib$LIBDIRSUFFIX/*
cp -aL ncbi/include $PKG/usr/include/ncbi
rm $PKG/usr/include/ncbi/{cn3d*,pcre*,vib*}
# Install and compress man pages
mkdir -p $PKG/usr/man
cp -aL ncbi/doc/man $PKG/usr/man/man1
rm $PKG/usr/man/man1/{Psequin.1,asnval.1,cleanasn.1,ddv.1,entrez2.1,\
fmerge.1,gbseqget.1,insdseqget.1,nps2gps.1,sortbyquote.1,spidey.1,\
trna2sap.1,trna2tbl.1,udv.1}
find $PKG/usr/man/man1 -type f -exec gzip -9 {} \;
# Install shared NCBI data
mkdir -p $PKG/usr/share/ncbi
cp -aL ncbi/data $PKG/usr/share/ncbi
# Install the documentation
DOCDIR=$PKG/usr/doc/$NAMEPKG-$VERSION
mkdir -p $DOCDIR
cp ncbi/README{,.htm} ncbi/VERSION $DOCDIR
cp ncbi/config/README $DOCDIR/README.config
cp ncbi/network/nsclilib/readme $DOCDIR/README.net-cfg
cp -aL ncbi/doc/* $DOCDIR
rm -rf $DOCDIR/man
# Install the default config file
install -D -m 644 $CWD/ncbirc $PKG/etc/ncbi/ncbirc.new
# Sanitize permissions
find $PKG -type d -exec chmod 755 {} \;
find $PKG -type f -exec chmod 644 {} \;
find $PKG/usr/bin -type f -exec chmod 755 {} \;
# Copy slack-desc and doinst.sh files
mkdir -p $PKG/install
install -m 644 $CWD/slack-desc $PKG/install/slack-desc
install -m 755 $CWD/doinst.sh $PKG/install/doinst.sh
# Package the tree
cd $PKG
mkdir -p $OUT
PACKAGING="
chown root:root . -R
/sbin/makepkg -l y -c n $OUT/$NAMEPKG-$VERSION-$ARCH-$BUILD.$EXT
rm -rf $PKG
rm -rf $TMP/$NAME
"
if type -p fakeroot ; then
echo "$PACKAGING" | fakeroot
else
su -c "$PACKAGING"
fi

1
ap/ncbi-toolkit/ncbi.tar.gz.sha1

@ -1 +0,0 @@
9727c13d94cc06cfe2f70148fa6bc5dfe011af50 ncbi.tar.gz

3
ap/ncbi-toolkit/ncbirc

@ -1,3 +0,0 @@
[NCBI]
DATA=/usr/share/ncbi/data

13
ap/ncbi-toolkit/slack-desc

@ -1,13 +0,0 @@
|-----handy-ruler------------------------------------------------------|
ncbi-toolkit: ncbi-toolkit (NCBI Software Development Toolkit)
ncbi-toolkit:
ncbi-toolkit: The NCBI Software Development Toolkit has been used for the
ncbi-toolkit: production and distribution of GenBank, Entrez, BLAST, and related
ncbi-toolkit: services by NCBI. It is freely available without restriction to
ncbi-toolkit: facilitate the use of NCBI by the scientific community.
ncbi-toolkit:
ncbi-toolkit:
ncbi-toolkit:
ncbi-toolkit:
ncbi-toolkit:
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